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Name of Collaboratory :


Biological Collaborative Research Environment (BioCoRE)


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URL :  

Collaboratory Status :

Operational   Start Date : 1998 End Date : not applicable Info Last Updated : Thu, Dec 8 2011 1:01am PST

Primary Collaboratory Function :

  Distributed Research Center  

Secondary Collaboratory Functions :

  Virtual Learning Community  

Domain(s) :

  structural biology, theoretical biophysics, interdisciplinary training

Brief Description of the Collaboratory :


BioCoRE is a collaborative work environment for biomedical research, research management and training. A resource-centered platform, BioCoRE offers scientists, working together or alone, a seamless interface to a broad range of local and remote technologies such as discipline-specific and general tools, data, and visualization solutions. To harness and streamline collaborative capabilities across temporal and physical boundaries in research and training, BioCoRE builds on the transparent use of and communication between technological resources (hardware and software) and databases. BioCoRE features powerful yet easy-to-use tools, among them co-authoring papers and other documents, running applications on supercomputers, sharing molecular visualization over the Internet, notifying project team members of recent project changes by email, chatting, keeping a lab book, and other practical features.


BioCoRE, a Biological Collaborative Research Environment for Structural Biology, is a web-based, tool-oriented collaboratory for biomedical research and training. Through BioCoRE, scientists have seamless, global access to their research data and collaborations. Designed to enhance the research process, BioCoRE improves the collaboration process between biomedical researchers located at either the same institution or at geographically distant places, and facilitates the transparent use of and communication between existing programs, tools, and databases. BioCoRE features capabilities such as chatting with collaborators, running applications on supercomputers, and remote and shared visualization of molecules over the Internet.

There are three main areas of BioCoRE:

1. The Workbench area includes collaborative access to visualization programs and a web-based interface for preparing, submitting, and monitoring supercomputer jobs and supports Globus and the Grid as a method of job submission.
2. The Notebook area furnishes the tools for logging, locating, and reviewing methodology, data, results, and annotations related to the ongoing projects.
3. The Documents interface includes access to a common file system that can be used by all areas of BioCoRE and supplies collaborators with a convenient way to share multi-author documents for publication.

Scientists are able to discuss their research in real time or time-delayed sessions via the conferencing tools. BioCoRE can be accessed via secure web browsers on Windows, Unix, Macintoshes, and PocketPC Personal Digital Assistants (PDAs).


Access to Instruments :

  High-powered computation for data analysis and visualization (both synchronously and asynchronously)  

Access to Information Resources :

  Data, communications, and analysis documentation archives  

Access to People as Resources :

  Close consultation between development team and users (tighly-controlled user feedback loop for user-centered design development), inter-collaborator communication  

Funding Agency or Sponsor :


Notes on Funding Agencies/Sponsors:
(NIH) (grant: PHS 5 P41 RR05969-04)


Notes on Participants/Organizations:
500 plus researchers involved in more than 100 projects as of (as of 9-3-02).


Communications Technology Used :

  The individual collaborators have several means to communicate with one another including:
1. chat rooms,
2. message boards,
3. audio and video conferencing,
4. shared white boards,
5. application sharing.
6. awareness mechanisms

Technical Capabilities :

  Management of technical resources
Access control/login facilities
Remote launch of computation, Simulation, modeling, visualization
Support for transition between synch and asynch
Directory of services/experts/resources, Shared calendars, Notification of events or a need by someone, Awareness of people's activities
Asynchronous object sharing
Index/metadata, General search capability, Vetted knowledge based of multiple authors, Common file space, Audit trail of events, "Handoff" authoring, Email/attachments
Asynchronous conversation
Threaded discussion, Audio capture and replay, Video capture and replay, Web forms, Chat archive, Email
Synchronous object sharing
Share visualization, Data conferencing
Synchronous conversation
Audio, Video, Instant messaging/chat
  Key Articles :  

Bhandarkar, M., Budescu, G., Humphrey, W. F., & Izaguirre, J. A. (1999). BioCoRE: A collaboratory for structural biology. in Bruzzone, A. G., Uhrmacher, A., & Page, E. H. (Eds.). Proceedings of the SCS International Conference on Web-based Modeling and Simulation, San Francisco, CA, 1999. (pp. 242-251). San Diego, CA: Society for Computer Simulation.

Finholt, T. A. (2003). Collaboratories as a new form of scientific organization Economics of Innovation and New Technology, 12(1), 5-25.


Project-reported performance data :

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